rs156823

Variant names:

• chr5-54043757-A-G
• rs156823
• NM_019087.3:c.462+69445T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-54043757-A-G
• chr5-54043757-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019087.3(ARL15):​c.462+69445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,878 control chromosomes in the GnomAD database, including 11,288 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (11288 hom., cov: 31)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 2 publications found

Genes affected

ARL15 (HGNC:25945): (ADP ribosylation factor like GTPase 15) Predicted to enable GTP binding activity and GTPase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL15	NM_019087.3	c.462+69445T>C		intron_variant	Intron 4 of 4	ENST00000504924.6	NP_061960.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL15	ENST00000504924.6	c.462+69445T>C		intron_variant	Intron 4 of 4	1	NM_019087.3	ENSP00000433427.1
ARL15	ENST00000502271.5	c.-76+69445T>C		intron_variant	Intron 4 of 4	1		ENSP00000473508.1
ARL15	ENST00000507646.2	c.462+69445T>C		intron_variant	Intron 4 of 4	5		ENSP00000432680.1
ARL15	ENST00000510591.6	n.535+69445T>C		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52788 AN: 151760 Hom.: 11288 Cov.: 31

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.358

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.348 AC: 52794 AN: 151878 Hom.: 11288 Cov.: 31 AF XY: 0.351 AC XY: 26081 AN XY: 74234

African (AFR) AF: 0.0875 AC: 3627 AN: 41452

American (AMR) AF: 0.472 AC: 7189 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3466

East Asian (EAS) AF: 0.395 AC: 2036 AN: 5150

South Asian (SAS) AF: 0.382 AC: 1841 AN: 4814

European-Finnish (FIN) AF: 0.464 AC: 4887 AN: 10526

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30225 AN: 67928

Other (OTH) AF: 0.354 AC: 745 AN: 2102

Alfa AF: 0.397 Hom.: 2393

Bravo AF: 0.342

Asia WGS AF: 0.331 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs156823; hg19: chr5-53339587;